1ENN

SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.135 

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This is version 1.2 of the entry. See complete history

Literature

Solvent organization in an oligonucleotide crystal. The structure of d(GCGAATTCG)2 at atomic resolution.

Soler-Lopez, M.Malinina, L.Subirana, J.A.

(2000) J.Biol.Chem. 275: 23034-23044

  • DOI: 10.1074/jbc.M002119200

  • PubMed Abstract: 
  • We describe the crystal structure of d(GCGAATTCG) determined by x-ray diffraction at atomic resolution level (0.89 A). The duplex structure is practically identical to that described at 2.05 A resolution (Van Meervelt, L., Vlieghe, D., Dautant, A., G ...

    We describe the crystal structure of d(GCGAATTCG) determined by x-ray diffraction at atomic resolution level (0.89 A). The duplex structure is practically identical to that described at 2.05 A resolution (Van Meervelt, L., Vlieghe, D., Dautant, A., Gallois, B., Précigoux, G., and Kennard, O. (1995) Nature 374, 742-744), however about half of the phosphate groups show multiple conformations. The crystal has three regions with different solvent structure. One of them contains several ordered Mg(+2) ions and can be considered as an ionic crystal. A second region is formed by a network of ordered water molecules with a polygonal organization that binds three duplexes. The third region is formed by channels of solvent in which very few ordered solvent molecules are visible. The less ordered phosphates are found facing this channel. The latter region provides a view of DNA with highly movable charges, both negative phosphates and counterions, without a precise location.


    Organizational Affiliation

    Departament d'Enginyeria Quimica, Universitat Politécnica de Catalunya, E-08028 Barcelona, Spain.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3')A,B9N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
O
Query on O

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A, B
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 21.938α = 90.00
b = 36.540β = 90.00
c = 52.728γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance